<div dir="ltr"><br><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Aug 14, 2014 at 1:42 PM, Smart Eagle <span dir="ltr"><<a href="mailto:wangykoo@gmail.com" target="_blank">wangykoo@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>Hi,</div><div> I just notice that GMX have plan to implement FMM in to GMX to calculate long-term forces for MD. You know PME will suffer FFT NxN all communactiom problems and FMM seemly can scale much better than FME. Indeed there have been a progrom called MODYLAS which have implement FMM to MD (J. Chem. Theory Comput. 2013, 9, 3201−3209<span style="line-height:0px"></span>). </div>
<div> I just want to know therotically, which is larger between FMM and PME for the time cost of long-term forces calculation in one MD steps in one nodes ? (means the basic calculation load for each method without consideration of communications between nodes). <span style="line-height:0px"></span><span style="line-height:0px"></span><span style="line-height:0px"></span></div>
</blockquote><div><br></div><div>Theoretically - it depends on the size of the simulation (which fixes N) and the quality of the implementations (which fix the prefactors in the asymptotic analysis of O(N) vs O(N log N)).</div>
<div><br></div><div>Practically - you could analyze the total flops on a given problem, but it would tell you little about the performance on a single node, because how well the implementation handles data flow is what dominates performance (now, and more so in the future). Adding inter-node parallelism makes that worse.</div>
<div><br></div><div>Mark</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>cheers up</div><div><br></div><br>--<br>
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